Darwin-related trojan email warning. Beagle blogger Richard has just sent this through:

A word of warning. Early this morning I received an email saying the following

lambstarpie@aol.com

hello. I'd like to offer my Darwin Souvenir pillows or photo on the site.. can you tell me where the place would be to best show this art to a needing public?

thank you,arribella pellicano

It contained a frankly bizarre attachment "origin of the species.bmp" showing a pillow with an image on it of a woman's naked torso and what appears to be a child wearing a chimp mask. Who is this joker? I thought."

So anyone who's blogging or has Darwin content on their website, watch out for this one.

Richard adds: I did some more research and ended up at a site which attempted a trojan attack on me: http://www.l-a-m-b-s-t-a-r.com (I have inserted dashes for safety purposes).

After having been twice driven back by heavy southwestern gales, Her Majesty's ship Beagle, a ten-gun brig, under the command of Captain Fitz Roy, R. N., sailed from Devonport on the 27th of December, 1831.

As dramatic opening sentences go, it's one of the best: Charles Darwin's account of the Beagle leaving England on her second and most famous voyage of adventure and discovery.

But Darwin isn't quite accurate when he describes Beagle as a ten-gun brig. Although that was indeed the generic name for such ships, and Beagle had been constructed as such, she was adapted for surveying work before her first voyage, and was, by the time Darwin set sail on her, strictly speaking, a bark. Keith S. Thompson explains the difference nice and succinctly in his book HMS Beagle: the ship that changed the course of history [ISBN: 0-75381-733-0]:

a brig has two masts and a bark three. On a brig both masts are square-rigged, and the mainmast also has a large fore-and-aft sail. On a bark the fore and mainmasts are square-rigged only; neither has a for-and-aft sail. The mizzenmast, by contrast only carries a fore-and-aft sail and no square sails.

Beagle only sailed once as a brig. Two months after she was launched at Woolwich Dockyard on 11th May, 1820, she sailed up the River Thames to take part in a naval precession in celebration of the coronation of King George IV. In so doing, she became the first man-of-war to pass fully rigged under the old London Bridge. After the celebrations, however, she was held in reserve—or in ordinary, as naval parlance has it—for the next five years.

In preparation for her first commission in 1825, Beagle returned to Woolwich to be re-rigged as a bark. The addition of a mizzenmast would make her more manoeuvrable, and enable her to sail closer to the wind—vital modifications for a ship which would soon be surveying the intricate and dangerous islands and channels of Tierra del Fuego. At the same time, a poop cabin was added to provide much-needed additional storage space, and to house a large charting table. It was this cabin that would house Charles Darwin and his cabin-mate John Lort Stokes during the second Beagle voyage several years later.

The addition of a poop cabin had a secondary benefit which was, in many ways, more important than its primary one: it added height to the stern of the ship, giving greater protection against heavy seas, and enabling the decks to drain more quickly. Unmodified ten-gun brigs had a reputation for foundering in heavy seas, earning them the alarming nickname of coffin brigs.

and we are promised a Big Day by the organizer. A veritable Niagra of people flooding through, one of whom will surely press a cheque for a million pounds into our hands, and add £250,000 in change for immediate expenses.

Like to buy a cup of coffee at the show: £2.85, which if you ask me should be a criminal offence.

The deadline for submission of entries to Open Lab 2008 is this Monday, 1 December, folks, so get crackin' and submit what you think are the best science blog posts of the year here, whether they be ours, yours or anyone else's, the point is to give some formal props to the best the science blogging community has to offer.

from a creationist. She took one of our jelly babies (we are resorting to shameless bribery to entice people to our stand), and quick as a flash Perry said, 'we'll need a donation for that'. She deposited 20 pence and told us she was a creationist, and that yes, the world and all herein was made in 6 days. So 1/20 millionth of the new Beagle wil be built with creationist money.

I sidled up to him and began the spiel. But I couldn't tell him anything about the voyage of the Beagle - he was director of photography on the Voyage of Charles Darwin, the 7 part series shot by the BBC in 1979 at a cost of £3 million (which was big money - it was the most expensive TV project ever). He had spent 18 months on and around the Marquesa directing the photography (as directors of photography will). A charming and modest man, I persuaded him to pose for a pic which I will post as soon as I can find my USB cable...

28 November 2008

here at the Boatshow. Just done a live interview with the famous Radio Caroline (to those not students of Brit counterculture, they broadcast the first pop music station into the UK from a vessel anchored in international waters, to the chagrin of the British establishment), and have recorded a piece for SailTV. The piece - recorded in front of the model Beagle - isn't up yet, but as soon as it is we'll post a link.

at the Sail, Power and Watersports Show in Earls Court exhibition centre on Warwick Road. There are all things boaty here, so if you're in, pop over and say hi. Our next-stand neighbours are Premier Ship Models who built the model of HMS Beagle for Darwin descendent Simon Keynes. The original is on our stand at the boat show (pictured right) so come and have a look, and stick a Darwin in our collection jar. And if you want a ship model - and no home is complete without at least one - talk to Premier and be sure to mention the Beagle Project sent you there.

25 November 2008

I really tried to come up with my own pithy title for this post. First I flirted with "Pascal's Wager: Undergrads can do big science", then I tried "Public participation in science: you're doin' it right" on for size, and I quite liked "Annotathon!" and "Please note: this metagenome has been annotated by undergrads", but in the end I decided I just couldn't beat the actual title of the paper, published in today's PLoS Biology, which describes something called the Annotathon, a clever bioinformatics teaching tool that doubles as a clever bioinformatics research tool.

Bioinformatics, the particular area of study/research in question, involves using computers to make sense of the mountains of biological data being ever more rapidly churned out by Sangerpyro-nanopore sequencing of the DNA of both single specimens (genomics) and multi-species samples (metagenomics).

The story began when researchers from Marseilles University, led by Pascal Hingamp, noticed that even as their lecture halls were heaving with undergraduates, so their data stockpiles were heaving with un-annotated DNA sequences extracted from mixed environmental samples. And that's when it happened--voila!--out of their piqued brains trundled the Annotathon!

The Annotathon involves training up undergrads to characterise DNA sequences and then setting them loose on a bunch of real stockpiled metagenomic sequences. The students have to use the internet to try and identify the organism the DNA comes from, for example, and what its biological function might be (if any).

In return for their much-needed help sorting out oodles of DNA data, the undergrads gain a practical knowledge of the work involved in doing bioinformatics and metagenomics, and, most importantly of all, they get to experience what it's like to do real research. That's the attraction of science after all, not the heavy tomes of factoids and boooring canned (and therefore inherently condescending) experiments, but rather the being at the edge of the envelope of human knowledge, and when you get some new data, however small it might be, for a little while you are the only person on Earth who knows what you know.

"The pace of research and the development of new areas of focus in biology are increasing at breathtaking speed. Unfortunately, exciting new areas of science typically do not appear in science classrooms and textbooks until many years after their inception. This pattern leaves undergraduate, and especially high school, biology education lagging behind scientific advances. The result is that too many students are never afforded opportunities to learn about the cutting-edge discoveries that make biology so exciting to professional scientists.

*snip*

"The birth of this exciting new field (described more fully below) provides the life sciences research and education communities with a powerful and rare opportunity. Metagenomics is so young, and the microbial world it seeks to characterize is so vast, that there is a real possibility that scientists, teachers, and students in many areas of science can work together to advance this field. By acting now to incorporate metagenomics into biology education and to utilize biology education to inform questions and future research paths for metagenomics, the life sciences community can begin to shift from the current situation, in which scientific advances take decades to reach the classroom, toward a system in which education and research are deliberately and strategically integrated with each other from the very beginning..."

Well, if that's not a strategy for re-invigorating science edcuation, I don't know what is. And for any die hard researchers out there who are still not convinced that undergrads should be allowed to contribute to research, consider this: the fact that this paper is in PLoS Biology shows that the students are producing high quality data; indeed their work ends up immortalised in the big public databases used daily by professional researchers (that'd be you).

Laboratory equipment wish list for the new Beagle:

DNA extraction robot

Nanopore sequencer

Annotathon

And with that, I think I might finally be triangulating towards a good title for this post ...nah.

Update 26th November: Many thanks to Dennis in comments who writes "I'm part of an undergraduate genomics project that has students involved in both finishing and annotation. It is run by Sally Elgin at Washington University which involves over 20 other colleges. We just published an article describing it in Science (Oct 31 issue). The conclusion, of course, is that it works." I would be delighted to write another blog post on that study, but sadly, despite working at a major scientific institution, I do not have online access to Science (ahem). So, perhaps Dennis (or someone else with access) would be so kind as to send me a pdf (karen at thebeagleproject dot com) of the Science article?Thanks, Ron!

23 November 2008

Please join us in making a very loud hullabaloo to welcome our new Beagle Project bloggers, Elke Watts and Richard Carter, both enthusiastic supporters of The HMS Beagle Project, who have kindly consented to lend their very considerable writing skillz to our humble weblog.

Yours truly and Beagle Project Blog founder Peter McGrath, gratefully receiving blogging tips from Chas. Darwin on the 14th of November. The quintessential collaborator, Chas made a not so subtle suggestion that we bring in a bit of fresh blood. Photo by Richard Carter.

Not only can Elke and Richard write circles around pretty much every anglophone around, except for maybe Peter, but they also have specific qualifications and working knowledge that complement our own very nicely indeed. Consider their abridged bios:

Elke Watts was raised in a sailing family, crewed aboard The St. Lawrence 2, a square rigged brigantine, has an Honours Bachelor of Science in Biology and Environmental Sciences from the University of Toronto, and just in case that wasn't impressive enough, her degree carried an emphasis on conservation biology.

Elke's also worked in the non-profit environmental sector, on various projects including environmental education, watershed restoration and taking school children on nature appreciation and tree planting expeditions. She's done PR and media relations, and written and published newsletters for environmental NGO's as well as seven major Canadian health care newsletters.

Richard Carter is a self-styled 'Darwin groupie' (I'd rather call him an amateur* Darwin scholar) who led a campaign to get Charles Darwin on the Bank of Enland £10 note.

And in case you hadn't noticed, Charles Darwin is now, in fact, on the Bank of England £10 note.

*pauses for effect*

As if that wasn't qualification enough for becoming a Beagle blogger, which of course it is, he works in IT (yessss!!), lives not terribly far away from Peter McGrath in Yorkshire and has a Natural Sciences degree from Durham University.

And so from Peter and myself, a warm 10-gun salute to welcome Elke and Richard aboard Her Majesty's Blog Beagle Project. We saves u a seat:

18 November 2008

Dr Jennifer Rohn, scientist, blogger and editor (to whom we are grateful for the lovely interview at LabLit) is now also a published novelist!

Her new book, Experimental Heart, is, according to Jennifer, "a light-hearted romantic thriller about post-docs under duress in a London research lab", which makes it exotic... not James Bond exotic, but exotic in the sense that real scientists, practicing real science, are strangely, and sadly, absent from pop culture.

Jennifer has a pea under her mattress about this omission, and so it's great to see her putting her passion into practice by making her characters real scientists.

Check out the rapturous blurbs:

"It is terrific...I was gripped from the first page to the last, which is unusual for me...[ the author has done] a brilliant job of weaving in so many aspects of science – experimental, social, and political – without making them intrusive."- Martin Raff, Molecular Biology of the Cell

"Science as it is practiced today can be conceptualized as a mystery story, or a love story, or a thriller. In EXPERIMENTAL HEART Rohn has made a brilliant synthesis of these three modes, resulting in a page-turner with depths, exploring the hope and danger of both bio-medicine and lab romance. In short, a true novel. Scientists who gave up reading fiction about science because it's never right – check this out. Non-scientists wondering what goes on it in that weird culture – find out here. By the end you'll be reading as fast as you can."- Kim Stanley Robinson, Hugo- and Nebula-award winning author of Red Mars, Antarctica and Forty Signs of Rain

We promised we'd be asking for your help, and here's our first request:

The Beagle Project needs a sharp, moving, great looking PR video to swell the hearts and burst the wallets of potential donors. We want tears running down cheeks and dropping on the cheque book, people.

Interested? Need more information or want a tidy overview of the Beagle Project to guide you on your creative film making journey? Email me at elke@thebeagleproject.com, and thank you to everyone who's made Youtube promos for the BP over the years, your efforts are greatly appreciated.

17 November 2008

an interesting post over at Mark Pallen's Rough Guide to Evolution blog about the two botanists who featured strongly in Charles Darwin's life: John Stevens Henslow and Joseph Hooker.

Henslow was responsible for Darwin being offered the unpaid naturalist berth on HMS Beagle, and the rest became history. Hooker's life story is absolutely extraordinary - how many people, far less botanists, can say they were imprisoned by a Rajah and realeased only because the British government threatened an invasion to secure one's freedom? Click over and acquaint yourself with both these remarkable scientists.

Cambridge University Library's website has some wonderful scans of artist Conrad Martens' sketchbooks, including numerous images from the second voyage of HMS Beagle (i.e. the Darwin voyage).

Martens joined Beagle in Montevideo in 1833, after the previous ship's artist, Augustus Earle, was taken ill. In many ways, these rough sketches are far more evocative than Martens' subsequent formal paintings.

Shown here is Slinging the monkey, Port Desire, which was painted on Christmas Day, 1833. It depicts Beagle (L) and Adventure (R) at anchor. In the foreground, six sailors play the naval game Swinging the Monkey, which involved hanging one of their number upside down until he was able to beat one of his taunting colleagues with a stick, after which, the two men swapped places.

16 November 2008

WHAT? In scientific and literary salons all over the world cups of tea shatter on the floor in reckless confusion. At the entrance to the Darwin's Big Idea exhibition in the Natural History Museum the first thing you see is a pair of dead birds reverentially displayed on a purple cushion.

In terms of evolutionary theory, stuff your finches (and there are 12 stuffed finches later in the exhibition), the Mockingbirds are what made Darwin intellectually jump out of the bath. In 1835, heading back to Britain, Darwin wrote that differences between mockingbirds on neighbouring Galapagos islands might 'undermine the stability of species'. If there is a recognizable eureka moment of evolutionary thought, this is it.

Of course, the the story is slightly more complicated. One of the birds was collected by Captain Robert Fitzroy, who to a sailor is the Banquo's ghost at this exhibition. To Darwin the academic plaudits, but Fitzroy did the heavy lifting, fitting Beagle out to the highest standards and skippering her safely round the world. And, as we have seen, playing more than a bit part in procuring the specimens that set Darwin on his path to the Linnean Society in 1858 and The Origin in 1859.

2009 is all about Darwin and the Origin, but Fitzroy was no mean observer and scientist himself, as anyone who has read his neglected account of the voyage will see. His attempt to reconcile what he saw with Genesis and the Flood, his vitriolic opposition to Darwin's theory of natural selection and melancholy suicide should not detract from that.

15 November 2008

Mike, who writes Tangled Up In Blue Guy (I've always been afraid to ask....) is one of our much appreciated blog peeps, and he's written a very kind pro-Beagle post here in response to Karen's Become A Beagle Projecteer post. He announces he will be adding a PayPal donation button to his blog to help collect funds for the Beagle Project, for which we are eternally grateful.

Inspired by Mike's gesture, we are working on a grab-and-go button to make it easy for anyone to help out in this way.

Thanks Mike!

(PS. Oh, and Peter and Karen do the heavy lifting over here, I am merely a crazed cheerleader, but shall be trying to shoulder a bit more of the load shortly.)

our big brothers in science NASA have successfully launched the Space Shuttle Endeavour. Endeavour's on her way to the International Space Station from which the rebuilt Beagle's progress around the world will be photographed. All the best for your time up there chaps, and as the Yorkshire outpost of the Beagle Project, I get an extra little thrill of pride that NASA named one of their Shuttles after Captain James Cook's Whitby built Endeavour. The Autralian built replica seen here entering Whitby Harbour.

And we hope to bring you the opening day of this great exhibition in as much detail as possible. Beagle Project Director of Science Karen James and Richard are going to liveblog the event. Not having a 270 mile ethernet cable, I shall fall back on my journalistic past and will be gathering visitors' impressions of the exhibition for a Beagle Project Podcast.

12 November 2008

Here at Beagle Project headquarters, we are weekly - if not daily - inspired and moved by acts of enthusiasm and support coming our way from those kindred hearts and minds from around the world who share our vision.

Many of you have already hit on creative ways to help us out - artists Diana Sudykas and Glendon Mellow have donated portions of their proceeds, bloggers have linked to us in their posts and sidebars, writers have made impassioned appeals online and in print, scientists have sent us their project ideas, movers and shakers have lent us their networks, classrooms have staged Beagle Project fund-raisers, and all kinds of people have donated to us through PayPal and bought Beagle Project gear in our shops. We have yet to be the recipients of proceeds from a bake sale or lemonade stand, but I'm sure it's not far off.

These unasked-for gifts of time and money are a great help to both our coffers and our spirits, and we will consider ourselves lucky if the trend continues. But, as Elke Watts recently asked me in an email that was so right-on it hurt, shouldn't we do something more organised to channel the goodwill of our enthusiastic supporters into real Beagle Project progress? And it was then that we came up with the idea of promoting and facilitating some coordinated action from this self-assembled group of supporters we've dubbed "The Beagle Projecteers".

The Beagle Projecteers are fans of the project who would be ready and willing to give us the £5 million we need to build the Beagle if only they had it, but in lieu of cash are keen to give of themselves. They are the ones who email us and ask, "how can I help"? And up until now we've only been able to ask that they spread the word and maybe donate via PayPal or buy something in our shop. No more. From now on we shall be able to provide an ever-growing, ever-changing list of tasks and requests for real volunteer action.

Stay tuned for our Cry to Action, and get ready to grab the serious Beagle Blog Bling we are creating for you, our friends and allies, to sport on your blogs and websites.

The Darwin exhibition is opening at the Natural History Museum in London this Friday, the 14th of November and your Beagle Project bloggers have a plan.

Peter and Beagle Project peep Richard Carter of ye olde Red Notebook and Friends of Charles Darwin fame will be making the long journey down to London from Yorkshire on Friday and we are going to have a Big, Old-fashioned Good Time viewing the Darwin exhibition together, drinking beer and...

...live-blogging! Yes, Richard the tech wizard has figured out how we can post to FriendFeed and stream that as a live blog over at Red Notebook on Friday.

9 November 2008

Update: I complained to BBC using their NewsWatch online feedback form and they corrected the online piece pronto, and on a Sunday too! Thanks, auntie!

Though we are, of course, delighted to see that our big Beagle Project-NASA press release has been covered by the BBC both on radio (fast forward to 1:20:00) and online, we are were just a leeeetle bit miffed that--despite our best efforts to correct them after the radio piece aired--they seemed to keep propagating the fairly serious misconception that we have already raised the money to rebuild HMS Beagle. We are in full on fundraising mode. We have not got anywhere close to the £5m we need yet, and it doesn't help our efforts when major news networks suggest that we have.

5 November 2008

HMS Beagle and Charles Darwin spent between June 1834 and July 1835 in Chile, or Chili as Darwin called it in his notebooks and diary of the time. His first impressions are very favourable: "The woods are incomparably more beautiful than those of Tierra del Fuego...excepting in Brazil I have never seen such an abundance of elegant forms."

Darwin made two of his great overland expeditions in Chile, first crossing the Andes then making a long trek north from Valparaiso to Copiapo. And on 3 March 1835 Charles Darwin's Beagle Diary records: "We felt, on board, a very smart shock of an earthquake: some compared the motion to that of a cable running out, & others to the ship touching on a Mud bank. — Capt. FitzRoy heard when on Mocha that the Sealers had experienced a succession of shocks during the last fortnight." His account of the earthquake and its aftermath is superb.

4 November 2008

The HMS Beagle Trust is an organisation with a healthy amount of political diversity amongst its directors and patrons. As such, your Beagle bloggers, however strong our personal preferences may be, have resisted the temptation to formally endorse a candidate for the US presidency on this blog.

We do note with vigorous interest and a certain amount of thinly veiled delight, however, that our great hero, Charles Darwin, has endorsed Mr. Obama.

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